X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=coverage.cpp;h=aebe66f1e0814f7a41fb9694403f87919fbcc660;hp=e7baf001fefe4d5de552c1cd6362eaa2b1333d2c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=42b802c0006d8b13bd5b27ea48d032a85d3f2102

diff --git a/coverage.cpp b/coverage.cpp
index e7baf00..aebe66f 100644
--- a/coverage.cpp
+++ b/coverage.cpp
@@ -2,39 +2,28 @@
  *  coverage.cpp
  *  Mothur
  *
- *  Created by Sarah Westcott on 3/9/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *  Created by Pat Schloss on 4/22/09.
+ *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  *
  */
 
 #include "coverage.h"
 
-//**********************************************************************************************************************
-vector< vector<float> > Coverage::getValues(FullMatrix*, float) {
+/***********************************************************************/
+EstOutput Coverage::getValues(SAbundVector* rank){
+
 	try {
-		globaldata = GlobalData::getInstance();
-		numGroups = globaldata->Groups.size();
-		
-		//initialize data
-		data.resize(numGroups);
-		for (int l = 0; l < data.size(); l++) {
-			data[l].push_back(0.0);
-		}
+		data.resize(1,0);
 
-		/**************************************/
-		//get the minumums for each comparision
-		/**************************************/
+		data[0] = 1. - rank->get(1) / (double)rank->getNumSeqs();
+		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Coverage", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
-//**********************************************************************************************************************
 
-	
\ No newline at end of file
+
+/***********************************************************************/